The oddest response I haven’t been able to find any threads on is the lights on the AVR programmer, when the programmer is first plugged in the green light is solid and the red light is flashing - after a few seconds both lights shut off and do not turn on again until programmer is unplugged and plugged back in.

Do you get the same behavior if you connect just the AVR Programmer to your computer without anything else connected to the programmer? If you have not already done so, can you try using a different USB cable and a different USB port to see if that changes anything?

If the AVR Programmer’s red LED is blinking, then the Baby Orangutan might not be powered properly by your external power supply. (See the description of the AVR Programmer’s LEDs under the “Module Pinout and Components” section of its user’s guide.) What are you using to power the Baby Orangutan?

It is possible that there could be a problem with your programmer. If you have a multimeter, can you measure the Baby Orangutan’s VDD line and the programmer’s VDD line and let us know what you get?